Per chromosome imputation report for cohort tmp.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 1.4.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 35589570 | 88.190 |
| 0.1 | 1219755 | 3.023 |
| 0.2 | 810372 | 2.008 |
| 0.3 | 620059 | 1.536 |
| 0.4 | 497543 | 1.233 |
| 0.5 | 408867 | 1.013 |
| 0.6 | 347624 | 0.861 |
| 0.7 | 293583 | 0.727 |
| 0.8 | 247936 | 0.614 |
| 0.9 | 320380 | 0.794 |
| 1.0 | 23 | 0.000 |
| Total | 40355712 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 27433132 | 67.978 |
| 0.1 | 720559 | 1.786 |
| 0.2 | 396639 | 0.983 |
| 0.3 | 320114 | 0.793 |
| 0.4 | 341848 | 0.847 |
| 0.5 | 430733 | 1.067 |
| 0.6 | 657402 | 1.629 |
| 0.7 | 1041614 | 2.581 |
| 0.8 | 1756496 | 4.353 |
| 0.9 | 7228707 | 17.912 |
| 1.0 | 28468 | 0.071 |
| Total | 40355712 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 2713439 | 88.3876 |
| 0.1 | 89996 | 2.9315 |
| 0.2 | 57477 | 1.8723 |
| 0.3 | 46013 | 1.4988 |
| 0.4 | 37698 | 1.2280 |
| 0.5 | 30435 | 0.9914 |
| 0.6 | 27340 | 0.8906 |
| 0.7 | 21879 | 0.7127 |
| 0.8 | 18796 | 0.6123 |
| 0.9 | 26857 | 0.8748 |
| 1.0 | 1 | 0.0000 |
| Total | 3069931 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 2093396 | 68.1903 |
| 0.1 | 55491 | 1.8076 |
| 0.2 | 30704 | 1.0002 |
| 0.3 | 25267 | 0.8230 |
| 0.4 | 26183 | 0.8529 |
| 0.5 | 33281 | 1.0841 |
| 0.6 | 50587 | 1.6478 |
| 0.7 | 80200 | 2.6124 |
| 0.8 | 134554 | 4.3830 |
| 0.9 | 538310 | 17.5349 |
| 1.0 | 1958 | 0.0638 |
| Total | 3069931 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 3004239 | 88.5622 |
| 0.1 | 101701 | 2.9981 |
| 0.2 | 64633 | 1.9053 |
| 0.3 | 50361 | 1.4846 |
| 0.4 | 38270 | 1.1282 |
| 0.5 | 32132 | 0.9472 |
| 0.6 | 29087 | 0.8575 |
| 0.7 | 22829 | 0.6730 |
| 0.8 | 21184 | 0.6245 |
| 0.9 | 27801 | 0.8195 |
| Total | 3392237 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 2328590 | 68.6447 |
| 0.1 | 59126 | 1.7430 |
| 0.2 | 31830 | 0.9383 |
| 0.3 | 25533 | 0.7527 |
| 0.4 | 27552 | 0.8122 |
| 0.5 | 33386 | 0.9842 |
| 0.6 | 50931 | 1.5014 |
| 0.7 | 82426 | 2.4298 |
| 0.8 | 141643 | 4.1755 |
| 0.9 | 608970 | 17.9519 |
| 1.0 | 2250 | 0.0663 |
| Total | 3392237 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 2489338 | 88.2151 |
| 0.1 | 87376 | 3.0964 |
| 0.2 | 56248 | 1.9933 |
| 0.3 | 42531 | 1.5072 |
| 0.4 | 34736 | 1.2309 |
| 0.5 | 29219 | 1.0354 |
| 0.6 | 24751 | 0.8771 |
| 0.7 | 20377 | 0.7221 |
| 0.8 | 16803 | 0.5955 |
| 0.9 | 20514 | 0.7270 |
| 1.0 | 1 | 0.0000 |
| Total | 2821894 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 1919954 | 68.0378 |
| 0.1 | 48409 | 1.7155 |
| 0.2 | 26776 | 0.9489 |
| 0.3 | 21548 | 0.7636 |
| 0.4 | 22678 | 0.8036 |
| 0.5 | 28252 | 1.0012 |
| 0.6 | 43574 | 1.5441 |
| 0.7 | 70686 | 2.5049 |
| 0.8 | 119655 | 4.2402 |
| 0.9 | 518045 | 18.3581 |
| 1.0 | 2317 | 0.0821 |
| Total | 2821894 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 2444008 | 87.6749 |
| 0.1 | 81445 | 2.9217 |
| 0.2 | 60234 | 2.1608 |
| 0.3 | 45786 | 1.6425 |
| 0.4 | 33643 | 1.2069 |
| 0.5 | 27624 | 0.9910 |
| 0.6 | 25015 | 0.8974 |
| 0.7 | 21948 | 0.7873 |
| 0.8 | 20060 | 0.7196 |
| 0.9 | 27817 | 0.9979 |
| 1.0 | 1 | 0.0000 |
| Total | 2787581 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 1885554 | 67.6412 |
| 0.1 | 47341 | 1.6983 |
| 0.2 | 25567 | 0.9172 |
| 0.3 | 20650 | 0.7408 |
| 0.4 | 22170 | 0.7953 |
| 0.5 | 27962 | 1.0031 |
| 0.6 | 42240 | 1.5153 |
| 0.7 | 69175 | 2.4815 |
| 0.8 | 119958 | 4.3033 |
| 0.9 | 525348 | 18.8460 |
| 1.0 | 1616 | 0.0580 |
| Total | 2787581 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 2290759 | 88.5089 |
| 0.1 | 76342 | 2.9497 |
| 0.2 | 52147 | 2.0148 |
| 0.3 | 40114 | 1.5499 |
| 0.4 | 31572 | 1.2199 |
| 0.5 | 24954 | 0.9642 |
| 0.6 | 22188 | 0.8573 |
| 0.7 | 18512 | 0.7153 |
| 0.8 | 15383 | 0.5944 |
| 0.9 | 16196 | 0.6258 |
| 1.0 | 1 | 0.0000 |
| Total | 2588168 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 1763151 | 68.1235 |
| 0.1 | 43688 | 1.6880 |
| 0.2 | 24252 | 0.9370 |
| 0.3 | 19406 | 0.7498 |
| 0.4 | 20460 | 0.7905 |
| 0.5 | 25511 | 0.9857 |
| 0.6 | 39307 | 1.5187 |
| 0.7 | 63248 | 2.4437 |
| 0.8 | 108111 | 4.1771 |
| 0.9 | 478855 | 18.5017 |
| 1.0 | 2179 | 0.0842 |
| Total | 2588168 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 2156804 | 87.6710 |
| 0.1 | 79488 | 3.2311 |
| 0.2 | 52857 | 2.1486 |
| 0.3 | 40821 | 1.6593 |
| 0.4 | 32773 | 1.3322 |
| 0.5 | 26436 | 1.0746 |
| 0.6 | 21956 | 0.8925 |
| 0.7 | 17809 | 0.7239 |
| 0.8 | 15115 | 0.6144 |
| 0.9 | 16052 | 0.6525 |
| Total | 2460111 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 1645996 | 66.9074 |
| 0.1 | 40353 | 1.6403 |
| 0.2 | 22237 | 0.9039 |
| 0.3 | 17817 | 0.7242 |
| 0.4 | 18604 | 0.7562 |
| 0.5 | 22926 | 0.9319 |
| 0.6 | 35135 | 1.4282 |
| 0.7 | 56156 | 2.2827 |
| 0.8 | 96860 | 3.9372 |
| 0.9 | 499269 | 20.2946 |
| 1.0 | 4758 | 0.1934 |
| Total | 2460111 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 2019910 | 88.2325 |
| 0.1 | 68609 | 2.9969 |
| 0.2 | 48590 | 2.1225 |
| 0.3 | 35253 | 1.5399 |
| 0.4 | 29755 | 1.2997 |
| 0.5 | 23670 | 1.0339 |
| 0.6 | 18935 | 0.8271 |
| 0.7 | 15953 | 0.6968 |
| 0.8 | 12645 | 0.5524 |
| 0.9 | 15985 | 0.6982 |
| Total | 2289305 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 1560178 | 68.1507 |
| 0.1 | 41044 | 1.7929 |
| 0.2 | 23169 | 1.0121 |
| 0.3 | 17750 | 0.7753 |
| 0.4 | 18555 | 0.8105 |
| 0.5 | 23518 | 1.0273 |
| 0.6 | 36492 | 1.5940 |
| 0.7 | 58533 | 2.5568 |
| 0.8 | 98326 | 4.2950 |
| 0.9 | 410592 | 17.9352 |
| 1.0 | 1148 | 0.0501 |
| Total | 2289305 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1988197 | 88.6517 |
| 0.1 | 64892 | 2.8935 |
| 0.2 | 44885 | 2.0014 |
| 0.3 | 31968 | 1.4254 |
| 0.4 | 27683 | 1.2344 |
| 0.5 | 22656 | 1.0102 |
| 0.6 | 18442 | 0.8223 |
| 0.7 | 15889 | 0.7085 |
| 0.8 | 13458 | 0.6001 |
| 0.9 | 14635 | 0.6526 |
| Total | 2242705 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 1540133 | 68.6730 |
| 0.1 | 37510 | 1.6725 |
| 0.2 | 21215 | 0.9460 |
| 0.3 | 16828 | 0.7503 |
| 0.4 | 18293 | 0.8157 |
| 0.5 | 22422 | 0.9998 |
| 0.6 | 33323 | 1.4858 |
| 0.7 | 54054 | 2.4102 |
| 0.8 | 91390 | 4.0750 |
| 0.9 | 405713 | 18.0903 |
| 1.0 | 1824 | 0.0813 |
| Total | 2242705 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1487517 | 88.2029 |
| 0.1 | 55269 | 3.2772 |
| 0.2 | 32574 | 1.9315 |
| 0.3 | 25271 | 1.4985 |
| 0.4 | 20587 | 1.2207 |
| 0.5 | 16220 | 0.9618 |
| 0.6 | 14551 | 0.8628 |
| 0.7 | 11891 | 0.7051 |
| 0.8 | 9962 | 0.5907 |
| 0.9 | 12627 | 0.7487 |
| 1.0 | 2 | 0.0001 |
| Total | 1686471 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 1137244 | 67.4334 |
| 0.1 | 31517 | 1.8688 |
| 0.2 | 16930 | 1.0039 |
| 0.3 | 13605 | 0.8067 |
| 0.4 | 14186 | 0.8412 |
| 0.5 | 17392 | 1.0313 |
| 0.6 | 27816 | 1.6494 |
| 0.7 | 45022 | 2.6696 |
| 0.8 | 75939 | 4.5028 |
| 0.9 | 306144 | 18.1529 |
| 1.0 | 676 | 0.0401 |
| Total | 1686471 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1692555 | 87.8108 |
| 0.1 | 60105 | 3.1183 |
| 0.2 | 40193 | 2.0852 |
| 0.3 | 28434 | 1.4752 |
| 0.4 | 25344 | 1.3149 |
| 0.5 | 20777 | 1.0779 |
| 0.6 | 16672 | 0.8650 |
| 0.7 | 14264 | 0.7400 |
| 0.8 | 12814 | 0.6648 |
| 0.9 | 16344 | 0.8479 |
| 1.0 | 1 | 0.0001 |
| Total | 1927503 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 1301616 | 67.5286 |
| 0.1 | 32472 | 1.6847 |
| 0.2 | 17956 | 0.9316 |
| 0.3 | 14207 | 0.7371 |
| 0.4 | 15288 | 0.7932 |
| 0.5 | 19002 | 0.9858 |
| 0.6 | 28722 | 1.4901 |
| 0.7 | 47390 | 2.4586 |
| 0.8 | 84387 | 4.3780 |
| 0.9 | 365335 | 18.9538 |
| 1.0 | 1128 | 0.0585 |
| Total | 1927503 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1702069 | 87.8719 |
| 0.1 | 57685 | 2.9781 |
| 0.2 | 36583 | 1.8887 |
| 0.3 | 31054 | 1.6032 |
| 0.4 | 24637 | 1.2719 |
| 0.5 | 20528 | 1.0598 |
| 0.6 | 18377 | 0.9487 |
| 0.7 | 14192 | 0.7327 |
| 0.8 | 12609 | 0.6510 |
| 0.9 | 19256 | 0.9941 |
| Total | 1936990 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 1308707 | 67.5640 |
| 0.1 | 34157 | 1.7634 |
| 0.2 | 18083 | 0.9336 |
| 0.3 | 14254 | 0.7359 |
| 0.4 | 14474 | 0.7472 |
| 0.5 | 17910 | 0.9246 |
| 0.6 | 29248 | 1.5100 |
| 0.7 | 49485 | 2.5547 |
| 0.8 | 84042 | 4.3388 |
| 0.9 | 364855 | 18.8362 |
| 1.0 | 1775 | 0.0916 |
| Total | 1936990 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1626923 | 88.0314 |
| 0.1 | 55740 | 3.0160 |
| 0.2 | 35699 | 1.9316 |
| 0.3 | 29810 | 1.6130 |
| 0.4 | 24035 | 1.3005 |
| 0.5 | 18940 | 1.0248 |
| 0.6 | 15692 | 0.8491 |
| 0.7 | 12677 | 0.6859 |
| 0.8 | 12900 | 0.6980 |
| 0.9 | 15696 | 0.8493 |
| 1.0 | 5 | 0.0003 |
| Total | 1848117 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 1249720 | 67.6213 |
| 0.1 | 32282 | 1.7468 |
| 0.2 | 17691 | 0.9572 |
| 0.3 | 14334 | 0.7756 |
| 0.4 | 15346 | 0.8304 |
| 0.5 | 19310 | 1.0448 |
| 0.6 | 29235 | 1.5819 |
| 0.7 | 47689 | 2.5804 |
| 0.8 | 81509 | 4.4104 |
| 0.9 | 339832 | 18.3880 |
| 1.0 | 1169 | 0.0633 |
| Total | 1848117 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1206984 | 87.1196 |
| 0.1 | 42966 | 3.1013 |
| 0.2 | 28142 | 2.0313 |
| 0.3 | 22842 | 1.6487 |
| 0.4 | 17215 | 1.2426 |
| 0.5 | 15864 | 1.1451 |
| 0.6 | 12687 | 0.9157 |
| 0.7 | 11376 | 0.8211 |
| 0.8 | 9670 | 0.6980 |
| 0.9 | 17686 | 1.2766 |
| 1.0 | 1 | 0.0001 |
| Total | 1385433 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 925753 | 66.8205 |
| 0.1 | 25070 | 1.8095 |
| 0.2 | 13384 | 0.9661 |
| 0.3 | 10674 | 0.7704 |
| 0.4 | 11299 | 0.8156 |
| 0.5 | 13981 | 1.0091 |
| 0.6 | 21928 | 1.5828 |
| 0.7 | 36318 | 2.6214 |
| 0.8 | 60109 | 4.3386 |
| 0.9 | 265833 | 19.1877 |
| 1.0 | 1084 | 0.0782 |
| Total | 1385433 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1116023 | 88.1162 |
| 0.1 | 39784 | 3.1412 |
| 0.2 | 26249 | 2.0725 |
| 0.3 | 18521 | 1.4623 |
| 0.4 | 15590 | 1.2309 |
| 0.5 | 11852 | 0.9358 |
| 0.6 | 10050 | 0.7935 |
| 0.7 | 9632 | 0.7605 |
| 0.8 | 7841 | 0.6191 |
| 0.9 | 10993 | 0.8680 |
| 1.0 | 1 | 0.0001 |
| Total | 1266536 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 862465 | 68.0964 |
| 0.1 | 23350 | 1.8436 |
| 0.2 | 12276 | 0.9693 |
| 0.3 | 9650 | 0.7619 |
| 0.4 | 10028 | 0.7918 |
| 0.5 | 12792 | 1.0100 |
| 0.6 | 19932 | 1.5737 |
| 0.7 | 31321 | 2.4730 |
| 0.8 | 53774 | 4.2458 |
| 0.9 | 230275 | 18.1815 |
| 1.0 | 673 | 0.0531 |
| Total | 1266536 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1005863 | 88.2944 |
| 0.1 | 32460 | 2.8493 |
| 0.2 | 22861 | 2.0067 |
| 0.3 | 17342 | 1.5223 |
| 0.4 | 13770 | 1.2087 |
| 0.5 | 11908 | 1.0453 |
| 0.6 | 8903 | 0.7815 |
| 0.7 | 7870 | 0.6908 |
| 0.8 | 6877 | 0.6037 |
| 0.9 | 11359 | 0.9971 |
| 1.0 | 2 | 0.0002 |
| Total | 1139215 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 779005 | 68.3809 |
| 0.1 | 21279 | 1.8679 |
| 0.2 | 11934 | 1.0476 |
| 0.3 | 9749 | 0.8558 |
| 0.4 | 10930 | 0.9594 |
| 0.5 | 13990 | 1.2280 |
| 0.6 | 20558 | 1.8046 |
| 0.7 | 30945 | 2.7163 |
| 0.8 | 51359 | 4.5083 |
| 0.9 | 188979 | 16.5885 |
| 1.0 | 487 | 0.0427 |
| Total | 1139215 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1139593 | 88.9406 |
| 0.1 | 37393 | 2.9184 |
| 0.2 | 22965 | 1.7923 |
| 0.3 | 18971 | 1.4806 |
| 0.4 | 14277 | 1.1143 |
| 0.5 | 12395 | 0.9674 |
| 0.6 | 10630 | 0.8296 |
| 0.7 | 9436 | 0.7364 |
| 0.8 | 6874 | 0.5365 |
| 0.9 | 8763 | 0.6839 |
| Total | 1281297 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 888172 | 69.3182 |
| 0.1 | 24011 | 1.8740 |
| 0.2 | 12732 | 0.9937 |
| 0.3 | 10183 | 0.7947 |
| 0.4 | 11339 | 0.8850 |
| 0.5 | 14191 | 1.1075 |
| 0.6 | 23118 | 1.8043 |
| 0.7 | 36692 | 2.8637 |
| 0.8 | 61907 | 4.8316 |
| 0.9 | 198615 | 15.5011 |
| 1.0 | 337 | 0.0263 |
| Total | 1281297 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 966744 | 88.6863 |
| 0.1 | 30561 | 2.8036 |
| 0.2 | 22907 | 2.1014 |
| 0.3 | 15799 | 1.4494 |
| 0.4 | 13001 | 1.1927 |
| 0.5 | 11413 | 1.0470 |
| 0.6 | 8981 | 0.8239 |
| 0.7 | 8030 | 0.7366 |
| 0.8 | 5856 | 0.5372 |
| 0.9 | 6780 | 0.6220 |
| Total | 1090072 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 748320 | 68.6487 |
| 0.1 | 22920 | 2.1026 |
| 0.2 | 12621 | 1.1578 |
| 0.3 | 10155 | 0.9316 |
| 0.4 | 11530 | 1.0577 |
| 0.5 | 15390 | 1.4118 |
| 0.6 | 22059 | 2.0236 |
| 0.7 | 33038 | 3.0308 |
| 0.8 | 51731 | 4.7456 |
| 0.9 | 161909 | 14.8531 |
| 1.0 | 399 | 0.0366 |
| Total | 1090072 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 968676 | 87.6824 |
| 0.1 | 34193 | 3.0951 |
| 0.2 | 23589 | 2.1352 |
| 0.3 | 17549 | 1.5885 |
| 0.4 | 13971 | 1.2646 |
| 0.5 | 11147 | 1.0090 |
| 0.6 | 8972 | 0.8121 |
| 0.7 | 8474 | 0.7670 |
| 0.8 | 6792 | 0.6148 |
| 0.9 | 11387 | 1.0307 |
| 1.0 | 5 | 0.0005 |
| Total | 1104755 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 745594 | 67.4895 |
| 0.1 | 20600 | 1.8647 |
| 0.2 | 11417 | 1.0334 |
| 0.3 | 9571 | 0.8663 |
| 0.4 | 9761 | 0.8835 |
| 0.5 | 13373 | 1.2105 |
| 0.6 | 20192 | 1.8277 |
| 0.7 | 30612 | 2.7709 |
| 0.8 | 51902 | 4.6981 |
| 0.9 | 191291 | 17.3152 |
| 1.0 | 442 | 0.0400 |
| Total | 1104755 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 766424 | 88.2414 |
| 0.1 | 29178 | 3.3594 |
| 0.2 | 19009 | 2.1886 |
| 0.3 | 13015 | 1.4985 |
| 0.4 | 9662 | 1.1124 |
| 0.5 | 8987 | 1.0347 |
| 0.6 | 6983 | 0.8040 |
| 0.7 | 5996 | 0.6903 |
| 0.8 | 4707 | 0.5419 |
| 0.9 | 4593 | 0.5288 |
| Total | 868554 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 590519 | 67.9887 |
| 0.1 | 16000 | 1.8421 |
| 0.2 | 9502 | 1.0940 |
| 0.3 | 7931 | 0.9131 |
| 0.4 | 9298 | 1.0705 |
| 0.5 | 12534 | 1.4431 |
| 0.6 | 18814 | 2.1661 |
| 0.7 | 27945 | 3.2174 |
| 0.8 | 43966 | 5.0620 |
| 0.9 | 131590 | 15.1505 |
| 1.0 | 455 | 0.0524 |
| Total | 868554 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 783418 | 88.5235 |
| 0.1 | 27416 | 3.0979 |
| 0.2 | 17765 | 2.0074 |
| 0.3 | 13663 | 1.5439 |
| 0.4 | 11044 | 1.2479 |
| 0.5 | 8826 | 0.9973 |
| 0.6 | 7642 | 0.8635 |
| 0.7 | 5930 | 0.6701 |
| 0.8 | 4673 | 0.5280 |
| 0.9 | 4606 | 0.5205 |
| Total | 884983 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 601536 | 67.9715 |
| 0.1 | 15868 | 1.7930 |
| 0.2 | 8898 | 1.0054 |
| 0.3 | 7358 | 0.8314 |
| 0.4 | 7701 | 0.8702 |
| 0.5 | 10542 | 1.1912 |
| 0.6 | 16387 | 1.8517 |
| 0.7 | 25260 | 2.8543 |
| 0.8 | 41643 | 4.7055 |
| 0.9 | 149500 | 16.8930 |
| 1.0 | 290 | 0.0328 |
| Total | 884983 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 466276 | 87.7653 |
| 0.1 | 16012 | 3.0139 |
| 0.2 | 10652 | 2.0050 |
| 0.3 | 8708 | 1.6391 |
| 0.4 | 7474 | 1.4068 |
| 0.5 | 6016 | 1.1324 |
| 0.6 | 4966 | 0.9347 |
| 0.7 | 4668 | 0.8786 |
| 0.8 | 3959 | 0.7452 |
| 0.9 | 2545 | 0.4790 |
| Total | 531276 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 362103 | 68.1572 |
| 0.1 | 10069 | 1.8952 |
| 0.2 | 5561 | 1.0467 |
| 0.3 | 4467 | 0.8408 |
| 0.4 | 4603 | 0.8664 |
| 0.5 | 6457 | 1.2154 |
| 0.6 | 9976 | 1.8777 |
| 0.7 | 14883 | 2.8014 |
| 0.8 | 24889 | 4.6848 |
| 0.9 | 88082 | 16.5793 |
| 1.0 | 186 | 0.0350 |
| Total | 531276 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 463772 | 88.4143 |
| 0.1 | 16097 | 3.0688 |
| 0.2 | 11034 | 2.1035 |
| 0.3 | 8370 | 1.5957 |
| 0.4 | 6865 | 1.3088 |
| 0.5 | 5467 | 1.0422 |
| 0.6 | 4603 | 0.8775 |
| 0.7 | 3909 | 0.7452 |
| 0.8 | 2695 | 0.5138 |
| 0.9 | 1732 | 0.3302 |
| Total | 524544 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 356493 | 67.9625 |
| 0.1 | 10897 | 2.0774 |
| 0.2 | 6318 | 1.2045 |
| 0.3 | 5029 | 0.9587 |
| 0.4 | 5451 | 1.0392 |
| 0.5 | 6853 | 1.3065 |
| 0.6 | 11016 | 2.1001 |
| 0.7 | 15837 | 3.0192 |
| 0.8 | 25721 | 4.9035 |
| 0.9 | 80781 | 15.4002 |
| 1.0 | 148 | 0.0282 |
| Total | 524544 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1090039 | 88.7629 |
| 0.1 | 35047 | 2.8539 |
| 0.2 | 23079 | 1.8793 |
| 0.3 | 17863 | 1.4546 |
| 0.4 | 13941 | 1.1352 |
| 0.5 | 11401 | 0.9284 |
| 0.6 | 10201 | 0.8307 |
| 0.7 | 10042 | 0.8177 |
| 0.8 | 6263 | 0.5100 |
| 0.9 | 10156 | 0.8270 |
| 1.0 | 2 | 0.0002 |
| Total | 1228034 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.0 | 838933 | 68.3151 |
| 0.1 | 27105 | 2.2072 |
| 0.2 | 15586 | 1.2692 |
| 0.3 | 14148 | 1.1521 |
| 0.4 | 16119 | 1.3126 |
| 0.5 | 19758 | 1.6089 |
| 0.6 | 26812 | 2.1833 |
| 0.7 | 34699 | 2.8256 |
| 0.8 | 53121 | 4.3257 |
| 0.9 | 180584 | 14.7051 |
| 1.0 | 1169 | 0.0952 |
| Total | 1228034 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering